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PubMed1995

2,3-Bisphosphoglycerate-independent phosphoglycerate mutase is conserved among different phylogenic kingdoms.

We have previously demonstrated that maize (Zea mays) 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (PGAM-i) is not related to 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. With the aid of specific anti-maize PGAM-i antibodies, we demonstrate here the presence of a closely related PGAM-i in other plants. We also describe the isolation and sequencing of a cDNA-encoding almond (Prunus amygdalus) PGAM-i that further demonstrates this relationship among plant PGAM-i. A search of the major databases for related sequences allowed us to identify some novel PGAM-i from different sources: plants (Arabidopsis thaliana, Oryza sativa and Antithamniom sp.), monera (Escherichia coli, Bacillus subtilis and Bacillus megaterium) and animals (Caenorhabditis elegans). All of these amino acid sequences share a high degree of homology with plant PGAM-i. These observations suggest that the PGAM-i from several biological kingdoms constitute a family of protein different from other proteins with related enzymatic function and arose from a common ancestral gene that has diverged throughout its evolution.

Amino Acid Sequence↗
PubMed1994

Neuropeptides and related nucleic acid sequences detected in peneid shrimps by immunohistochemistry and molecular hybridizations.

The neurosecretory cells in the eyestalks of Penaeus indicus and P. vannamei were studied by immunocytochemistry using polyclonal antisera raised against purified Homarus americanus neuropeptides. Cross-reactions between two H. americanus anti-crustacean hyperglycemic hormone antisera and Penaeus neurosecretory material were observed. The specific anti-vitellogenesis inhibiting hormone antiserum only showed an immunological reaction in the nervous tract and the sinus gland of Penaeus, suggesting a progressive exposure of a characteristic epitope which was amenable to immunological detection. Molecular hybridizations were performed in P. indicus and P. vannamei with a digoxigenin tailed 23mer oligonucleotide probe deduced from two partial sequences of uncharacterized, purified P. duorarum neuropeptides. Two distinct clusters of positive cells were observed by in situ hybridization experiments in the medulla terminalis ganglionic X-organ. Classical control tests gave negative results. Northern and Southern blot analyses were performed with the same tailed probed and allowed the determination of molecular weights for the mRNA and for a DNA restriction fragment (Pst 1), 1.7 kb and 200 bp, respectively. These observations show the existence of a strong homology between the P. duorarum sequence (selected for synthesizing the probe), and some P. indicus and P. vannamei neuropeptide sequence(s). Heterologous antisera were tested in other Arthropods to complete our analyses. In the centipede Lithobius forficatus and the scorpion Euscorpius carpathicus, the anti-crustacean hyperglycemic hormone antiserum induced a strong cross-reaction. A monoclonal anti-bombyxin-1 antiserum showed an immunoreaction in the neurosecretory system of the insects Tenebrio molitor and Labidura riparia. In contrast, the anti-bombyxin-1 antiserum did not react either in Penaeus or in Lithobius, and the Homarus hyperglycemic hormone antiserum did not react in the insects that were tested. A comprehensive view of these observations is discussed in relation to a divergence in Arthropod evolution.

Animals↗
PubMed1988

Molecular cloning and characterization of homeo-box-containing genes from Atlantic salmon.

As the most primitive group among vertebrates, fish might serve as a model system when studying the genetic regulation of embryogenesis in higher animals. To identify genes important for early development, we have constructed a genomic library from Atlantic salmon (Salmo salar) and screened it with homeobox-containing probes from Drosophila melanogaster. Five different salmon homeoboxes were isolated. Two of these were located in the same clone, separated by only 7.5 kb. This demonstrates the presence of clustered homeobox genes in fish. The two clustered homeoboxes were sequenced and shown to be closely related to the ANT-C/BX-C class of Drosophila, being about 80% homologous to the Ultrabithorax gene (Ubx) homeobox. One of the clustered genes appears to be the salmon equivalent of the mouse Hox-2.1 gene, indicating that some of the vertebrate homeobox-containing genes are conserved in evolution. A more diverged homeobox that shares only 60% homology with Ubx, was also sequenced. In analogy to Drosophila, therefore, the salmon genome contains more than one class of homeoboxes. In addition, Northern-blot experiments demonstrated that two of the homeobox genes are expressed in salmon embryos, suggesting their importance for proper development.

Amino Acid Sequence↗
PubMed2005

Identification and expression profile of the ID gene family in the rainbow trout (Oncorhynchus mykiss).

ID proteins are negative regulators of basic helix-loop-helix transcription factors governing growth and development in mammals. However, little is known about the ID gene function and expression in fish. We report the identification and characterization of two new rainbow trout ID genes (ID1D and ID2B) and extend our expression analyses of two previously identified ID genes (ID1A and ID2A). Phylogenetic analyses indicate an evolutionary relationship between ID1A and ID1D and between ID1B and ID1C, suggesting a mechanism of divergence throughout salmonid evolution. To access the expression of these genes in adult and developing fish, we measured the relative transcript abundance of four ID1 and two ID2 genes by real-time PCR. ID1 transcripts were expressed in a variety of tissues and the ID1 paralogues showed similar patterns of expression, whereas the ID2 paralogues were differentially expressed. To access the role of the ID genes during embryonic development, gene expression was measured at early (day 0 and day 2), mid (day 9 and day 18) and late (day 30 and day 50) embryonic development. ID1A and ID1D expression remained unchanged throughout embryonic development, while ID1B and ID1C were lowest during early, highest at mid, and decreased during late embryonic development. The ID2 transcripts revealed the highest expression in unfertilized eggs and day 2 embryos, and remained low throughout the remainder of embryonic development. The sequence analyses and gene expression patterns implicate gene and genome duplication in rainbow trout ID gene evolution and suggest an extensive role for the IDs in rainbow trout growth and development.

Animals↗
PubMed2004

Discovery of a highly-specialized plesiadapiform primate in the early-middle Eocene of northwestern Africa.

In this paper we report the first occurrence of an endemic African plesiadapiform primate from the early-middle Eocene locality of Glib Zegdou (Hammada du Dra, Algeria). Dralestes (new genus) is a very specialized taxon, and its closest known relative is the enigmatic and controversial genus Azibius from Gour Lazib (Hammada du Dra). We group both together as the Azibiidae (new rank). Dralestes provides the first evidence of the upper dentition in this group. Some critical dental characters, such as a postprotocingulum on upper teeth, consistently reveal a primate status for the azibiids. Dralestes exhibits, however, a very unusual configuration of the upper molars by the enlarged parastyle, the lack of a metaconule, and the ectoloph structure (preparacrista, centrocrista and postmetacrista are aligned in a high blade-like structure). The apparent dental specializations of both lower premolars and molars of azibiids (exaenodonty, large P(4) bearing sharp apical cusps, and M(1) having a highly elongated trigonid) point to potential relationships with Chronolestes and carpolestid plesiadapiforms. A phylogenetic analysis, performed on 55 dental characters scored for 19 primate genera, clarifies the euprimate status of Altiatlasius, and thus indicates that azibiids are the only known plesiadapiforms from Africa. Azibiids are the sister group of the clade carpolestids/Chronolestes in the superfamily Plesiadapoidea. However, the azibiids differ fundamentally from carpolestids by the combined lack of a centroconule and multiple buccal cusps on P(4). The exact position of both Chronolestes and azibiids in the plesiadapoids appears difficult to resolve. A basal position of Chronolestes in this superfamily cannot be ruled out because it exhibits a simple morphology of I(1) and no conule on P(3). Considering this ad hoc hypothesis, azibiids are found to lie outside a clade including carpolestids/plesiadapids/saxonellids, and they are the sister group to Chronolestes. The clade including the carpolestid, saxonellid, and plesiadapid families is characterized by the occurrence of a centroconule on P(3-4). The lack of this trait in Dralestes and Chronolestes could mean that azibiids are basal plesiadapoids that diverged before the evolution of the common ancestor of the three derived plesiadapoid families, i.e. at least around the Paleocene-Eocene boundary or more probably during the Paleocene. The report of the first offshoot in Africa of plesiadapoids enhances the role of Africa in the early primate radiation.

Algeria↗
PubMed2004

Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5.

Sec1/Mun18-like (SM) proteins and soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) play central roles in intracellular membrane fusion. Diverse modes of interaction between SM proteins and SNAREs from the syntaxin family have been described. However, the observation that the N-terminal domains of Sly1 and Vps45, the SM proteins involved in traffic at the endoplasmic reticulum, the Golgi, the trans-Golgi network and the endosomes, bind to similar N-terminal sequences of their cognate syntaxins suggested a unifying theme for SM protein/SNARE interactions in most internal membrane compartments. To further understand this mechanism of SM protein/SNARE coupling, we have elucidated the structure in solution of the isolated N-terminal domain of rat Sly1 (rSly1N) and analyzed its complex with an N-terminal peptide of rat syntaxin 5 by NMR spectroscopy. Comparison with the crystal structure of a complex between Sly1p and Sed5p, their yeast homologues, shows that syntaxin 5 binding requires a striking conformational change involving a two-residue shift in the register of the C-terminal beta-strand of rSly1N. This conformational change is likely to induce a significant alteration in the overall shape of full-length rSly1 and may be critical for its function. Sequence analyses indicate that this conformational change is conserved in the Sly1 family but not in other SM proteins, and that the four families represented by the four SM proteins found in yeast (Sec1p, Sly1p, Vps45p and Vps33p) diverged early in evolution. These results suggest that there are marked distinctions between the mechanisms of action of each of the four families of SM proteins, which may have arisen from different regulatory requirements of traffic in their corresponding membrane compartments.

Animals↗
PubMed2006

Functional analysis of Trypanosoma brucei PUF1.

The genomes of Trypanosoma brucei, Leishmania major and Trypanosoma cruzi each encode 10 proteins with PUF domains. PUF domain proteins from yeast and metazoa have been shown to bind RNA and to regulate mRNA stability and translation. Phylogenetic analysis suggested that the PUF proteins were duplicated and diverged early in evolution, and that most PUF proteins were lost during the evolution of mammals. Depletion of any of the first nine T. brucei PUF protein mRNAs by RNA interference had no effect on cell growth; combined depletion of PUF1 and PUF3, PUF3 and PUF4, and PUF1 and PUF4 mRNAs also had no effect. In conflict with a previous report, procyclic trypanosomes lacking PUF1 genes grew normally and we could find no evidence that PUF1 is required for growth of trypanosomes in culture. Depletion or elimination of PUF1 mRNA did not affect the abundances of any other mRNAs, as detected in microarray analysis, and also had minimal effects on the proteome. (In control experiments, treatment of bloodstream and procyclic cells with 100 ng/ml tetracycline also had no detectable effects on the transcriptome and proteome.) PUF1 preferentially bound to retroposon RNAs and was not associated with polysomes. We suggest that, as in yeast, there may be functional redundancy among the Kinetoplastid PUF proteins, or they may be involved in fine-tuning gene expression together with other proteins. Alternatively, PUF proteins may be needed in differentiating trypanosomes or in non-culturable life-cycle stages.

Animals↗
PubMed2006

Molecular cloning and characterization of FSH and LH receptors in Atlantic salmon (Salmo salar L.).

Two cDNAs encoding the FSH receptor (FSHR) and the LH receptor (LHR) from Atlantic salmon (Salmo salar) were cloned and characterized. The predicted protein sequence for FSHR comprises a mature protein of 635 amino acids (aa) and a signal peptide of 23aa, and for LHR a mature protein of 701aa and a signal peptide of 27aa. Multiple sequence alignment of Atlantic salmon FSHR and LHR with gonadotropin receptor sequences of available teleosts and representative vertebrates revealed high sequence homology with other salmonids (97-98% for both receptors); amino acid identities ranged from 59 to 67% for FSHR and 47-79% for LHR compared with other teleosts, and between 50 and 52% compared with other vertebrates. The salmon FSHR and LHR showed the typical characteristics of glycoprotein receptors, including a long N-terminal extracellular domain (ECD), seven transmembrane domains and a short C-terminal intracellular domain. The ECD of the Atlantic salmon FSHR and LHR were composed of nine imperfect leucine-rich repeats forming the potential recognition sites for the corresponding hormone. The comparative analysis of the recognition sites in the Atlantic salmon gonadotropin receptors with the corresponding sites in the human receptors showed that the nature of the residues involved in the key contacts with the glycoprotein alpha-subunit were highly conserved. In contrast the recognition sites for the specific beta-subunits showed clear differences between the two salmon gonadotropin receptors and the human receptors. In the salmon LHR the recognition sites for the LH beta-subunit were relatively conserved, while the recognition sites for the FSH beta-subunit in the salmon FSHR showed a higher divergence, suggesting different evolution rates for the two teleost gonadotropin receptors. Both FSHR and LHR were mainly expressed in the ovary and testis, but were also detected at low abundance in extra-gonadal tissues such as gills, brain, liver and heart.

Amino Acid Sequence↗
PubMed2004

Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters.

Primate genomes contain a very large number of short interspersed GC-rich repeats of the Alu family, which are abundant in introns and intergenic spacers but also present in 5' flanking regions of genes enriched in binding motifs (BMs) for transcription factors and frequently containing CpG islands. Here we studied whether CpG islands located in promoters of human genes overlap with Alu repeats and with clusters of BMs for the zinc-finger transcription factors Sp1, estrogen receptor alpha, and YY1. The presence of estrogen-response elements in Alu was shown earlier and here we confirm the presence in the consensus Alu sequence of the binding sites for Sp1 and YY1. Analyzing >5000 promoters from the two databases we found that Alu sequences are underrepresented in promoters compared to introns and that approximately 4% of CpG islands located within the -1000 to +200 segments of human promoters overlap with Alu repeats. Although this fraction was found to be lower for proximal segments of promoters (-500 to +100), our results indicate that a significant number (>1000) of all human genes may be controlled by Alu-associated CpG islands. Analysis of clustering of potential BMs for the indicated transcription factors within some promoters also suggests that the Alu family contributed to the evolution of transcription cis-regulatory modules in the human genome. It is important that among Alu sequences overlapping with CpG islands in promoters a large fraction of members of the old Alu subfamilies is found, suggesting extensive retroposon-assisted regulatory genome evolution during the divergence of the primates.

5' Flanking Region↗
PubMed1986

Multiple sequences in the Drosophila melanogaster U3 RNA gene are homologous to vertebrate U3 RNA.

We have cloned and sequenced a DNA fragment from the genome of Drosophila melanogaster which is homologous to Novikoff hepatoma (rat) small nucleolar U3 RNA. DNA sequence analysis shows that the regions of homology between the cloned DNA and rat U3 RNA are distributed over the entire length of the molecule and the total homology of linear sequence is 53%. The present finding supports the generalization that U3 RNA has been evolutionally conserved but diverges between mammals and invertebrates. This clone contains the upstream and downstream sequences required for the efficient and correct transcription of small nuclear RNAs. The secondary structure proposed for the U3 RNA sequence deduced from the cloned DNA is similar in general topography to that reported for rat U3 RNA (Bernstein et al., ref. 23).

Animals↗
PubMed2002

Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin.

Abalone sperm use 16 kDa lysin to create a hole in the egg vitelline envelope (VE) by a species-specific, nonenzymatic mechanism. To create the hole, lysin binds tightly to VERL (the VE receptor for lysin), a giant, unbranched glycoprotein comprising 30% of the VE. Binding of lysin to VERL causes the VERL molecules to lose cohesion and splay apart creating the hole. Lysin and VERL represent a cognate pair of gamete recognition proteins, one male the other female, which mediate fertilization. The coevolution of such cognate pairs may underlie the establishment of species-specific fertilization which could be a component of the mechanism to achieve reproductive isolation and hence new species. Here we present the full-length cDNA sequence (11,166 bp) of VERL from the red abalone (Haliotis rufescens). There are 42 amino acids from the start Met residue to the beginning of the first 'VERL repeat'. Most of VERL (9981 bp; 89.4%) consists of 22 tandem repeats of a approximately 153 amino acid sequence that is predicted to be beta-sheet. The last VERL repeat is followed by 353 non-repeat amino acid residues containing a furin cleavage site (RTRR), a ZP domain and a hydrophobic COOH-terminus with a 3' UTR of only 10 nucleotides. VERL repeats 3-22 have been subjected to concerted evolution and consequently have almost identical sequences. Curiously, comparisons of repeats from other species shows that repeats 1 and 2 of red abalone VERL have not been subjected to concerted evolution since the divergence of the red species from the other six California species.

Amino Acid Sequence↗
PubMed2003

Translational machinery of channel catfish: II. Complementary DNA and expression of the complete set of 47 60S ribosomal proteins.

Ribosomal protein genes have become widely used as markers for phylogenetic studies and comparative genomics, but they have not been available in fish. We have cloned and sequenced a complete set of all 47 60S ribosomal protein cDNAs from channel catfish (Ictalurus punctatus), of which 43 included the complete protein encoding regions. Most ribosomal protein mRNAs in channel catfish are highly similar to their mammalian counterparts. However, L4, L14, and L29 are significantly shorter in channel catfish than in mammals due to deletions in the 3' end of the gene. Two distantly related L5 cDNAs, L5a and L5b, were found in channel catfish. L5a is more similar to L5 in other vertebrates, while L5b showed significant levels of divergence, suggesting independent evolution of the two L5-encoding genes. The 47 ribosomal protein genes are generally highly expressed and together account for 11-14% of overall gene expression, depending on the tissues. Expression levels were highly variable both within a single tissue among different ribosomal protein genes, and among tissues with regard to a single ribosomal protein gene. Strong tissue preference expression was also observed for some ribosomal proteins. This set of ribosomal protein gene sequences represents one of the most complete sets from any single organism and will aid in fish phylogenetic and comparative genomic studies.

Alternative Splicing↗
PubMed1998

Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria.

We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity < 90%) in the data sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97-100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in evolution into an exclusive freshwater cluster and an exclusive marine cluster, the so-called SAR11 cluster. The detection of these three bacterial clades in lakes distinguished by geographic distance as well as physical and chemical diversity suggests that these organisms are dispersed globally and that they possess unique functional capabilities enabling successful competition in a wide range of freshwater environments.

Actinomycetales↗
PubMed2000

Vnd/nkx, ind/gsh, and msh/msx: conserved regulators of dorsoventral neural patterning?

Expression of vnd in ventral, ind in intermediate, and msh in dorsal columns of fly neurectoderm, and of homologous gene families in corresponding domains of vertebrate neurectoderm, suggests that elements of dorsoventral neural patterning have been evolutionarily conserved. However, upstream signaling pathways regulating this columnar gene expression pattern appear to have diverged significantly throughout evolution. In addition, while recent loss-of-function studies in flies and mice indicate that these three genes may have a conserved role in regional specification, there is no obvious conservation of the particular cell fates deriving from corresponding domains. The three-column expression pattern may thus represent a developmental mechanism that is more resistant to evolutionary changes than genetic events upstream or downstream of it.

Animals↗
PubMed2002

Dystrophin and functionally related proteins in the nematode Caenorhabditis elegans.

We investigated the function of dystrophin in the nematode Caenorhabditis elegans. Although nematodes and mammals diverged early in evolution, their muscles share many structural and molecular features, thus rendering C. elegans relevant as a model to study muscle function. Dystrophin, dystrobrevin, dystroglycans and several sarcoglycans have conserved homologues in the genome of C. elegans. The major strength of the model comes from its genetic tractability, which allows the quick and easy manipulation of gene expression, either to inactivate genes, or to create transgenic animals. Over the last 2 years, work on C. elegans dystrophin has led to the identification of a putative new member of the dystrophin-glycoprotein complex, and has brought additional data suggesting that dystrophin mutations affect ion channel function.

Animals↗
PubMed1999

Identification of a rice APETALA3 homologue by yeast two-hybrid screening.

A cDNA clone OsMADS16 was isolated from the rice young inflorescence cDNA expression library by the yeast two-hybrid screening method with OsMADS4 as bait. We have previously shown that the OsMADS4 gene is a member of the PI family and that the MADS-box gene is involved in controlling development of the second and third whorls of rice flowers. The sequence comparison indicated that OsMADS16 belongs to the AP3 family. The OsMADS16 protein contains a PI-derived motif, FAFRVVPSQPNLH, that is a conserved sequence in AP3 family genes at the C-terminal region. In addition, OsMADS16 contains a paleoAP3 motif, YGGNHDLRLG, downstream of the PI-derived motif. The paleoAP3 motif is a consensus sequence in the C-terminal region of the AP3 family genes of lower eudicot and magnolid dicot species. RNA blot analysis showed that the OsMADS16 gene was expressed in the second and third whorls, whereas the OsMADS4 transcripts were present in the second, third, and fourth whorls. These expression patterns of the OsMADS16 and OsMADS4 genes are very similar to those of AP3 and PI, respectively. In the yeast two-hybrid system, OsMADS4 interacted only with OsMADS16 among several rice MADS genes investigated, suggesting that OsMADS4 and OsMADS16 function as a heterodimer in specifying sepal and petal identities. The OsMADS16 protein displayed transcription activation ability in yeast, whereas AP3 did not. It was also shown in yeast that OsMADS16 interacted with PI whereas OsMADS4 did not interact with AP3. These differences between OsMADS16 and AP3 indicate that the functions of the AP3 family genes of monocots and dicots diverged during molecular evolution processes of the B function genes. Deletion analysis showed that the 155-200 amino acid region of the OsMADS16 protein plays an important role in the transcription activation ability.

Amino Acid Sequence↗
PubMed1978

Comparison of cloned rabbit and mouse beta-globin genes showing strong evolutionary divergence of two homologous pairs of introns.

Cloned beta-globin genes of both mouse and rabbit each contain a large and a small intervening sequence (intron) of about equal length at precisely the same positions relative to the coding sequence. The homologous introns show some sequence similarity, particularly at the junctions with the coding sequence. They most probably arose from a common ancestral sequence and diverged substantially during evolution.

Animals↗
PubMed1987

Intraspecific and interspecific variation in the sequence and abundance of highly repeated DNA among mosquitoes of the Aedes albopictus subgroup.

Interspecific variation in abundance of highly repeated DNA sequences has been examined in three species of the Aedes scutellaris and three species of the A. albopictus subgroup of the A. scutellaris group. Sequences from a population of A. albopictus were hybridised with whole genomic content from other species and strains. Copy number estimates were determined by dot-blot hybridisation. Variation in sequence abundance between strains of A. albopictus was as great as between it and the other six species. Two clusters were formed by principal components analysis, each of which contains populations of A. albopictus. Copy numbers of highly repeated sequences do not correlate with genome size. The results indicate extensive sequence divergence and rapid evolution. These findings are discussed in relation to the importance of concerted evolution and natural selection in the evolution of the species group.

Aedes↗